How to model blebs like structure as in lungs alveoli?
Would something like this work? Here is the .blend file.



Here is what I did:
1. Made 1 UV Sphere
2. Made 1 Plain Axis Empty
3. Added the following modifiers in order: Displace (Object: Empty), Solidify (Thickness 0.1 m), and Boolean (see step 5)
4. Duplicated these UV Spheres. I did separate objects, but going into edit mode and duplicating there would work as well.
5. Add the shape you want to be the cutout.
6. Select a sphere and in the Boolean modifier, set the object to your cut out object and have the operation be "Difference"
7. If doing separate objects, select the other spheres and then the sphere with the Boolean object selected last. Hit CTRL + L and link Modifiers.

Tada!

Instead of manually creating each blob, you can also make a particle system then convert the particle system to a mesh and do steps 2-7 (maybe it would work without converting to a mesh too).
If you have any questions, or I did not make quite what you are looking for, let me know.